def __init__(self, *args, **kwargs):
QWidget.__init__(self, *args, **kwargs)
self.simulationInterval = None
self.updateInterval = None
self.runTime = None
self.modelRoot = None
self.dataRoot = None
self.runner = Runner()
self.resetAndRunAction = None
self.stopAction = None
self.continueAction = None
self.preferences = preferences
self.currentSimulationRuntime = None
self.modelType = None
self.simulationRuntime = None
self.schedulerToolBar = self.getSchedulerToolBar()
self.runner.simulationProgressed.connect(
self.updateCurrentSimulationRuntime)
self.continueFlag = False
self.preferences.applyChemicalSettings.connect(self.resetSimulation)
def __init__(self, *args, **kwargs):
QtGui.QWidget.__init__(self, *args, **kwargs)
self.simulationInterval = None
self.updateInterval = None
self.runTime = None
self.modelRoot = None
self.dataRoot = None
self.runner = Runner()
self.resetAndRunAction = None
self.stopAction = None
self.continueAction = None
self.preferences = preferences
self.currentSimulationRuntime = None
self.modelType = None
self.simulationRuntime = None
self.schedulerToolBar = self.getSchedulerToolBar()
self.runner.simulationProgressed.connect(self.updateCurrentSimulationRuntime)
self.continueFlag = False
self.preferences.applyChemicalSettings.connect(self.resetSimulation)
class SchedulingWidget(QtGui.QWidget):
"""Widget for scheduling.
Important member fields:
runner - object to run/pause/continue simulation. Whenever
`updateInterval` time has been simulated this object sends an
`update()` signal. This can be connected to other objects to
update their data.
SIGNALS:
resetAndRun(tickDt, tickTargets, simtime, updateInterval)
tickDt: dict mapping tick nos to dt
tickTargets: dict mapping ticks to target paths
simtime: total simulation runtime
updateInterval: interval between update signals are to be emitted.
simtimeExtended(simtime)
emitted when simulation time is increased by user.
"""
resetAndRun = QtCore.pyqtSignal(dict, dict, float, float, name='resetAndRun')
simtimeExtended = QtCore.pyqtSignal(float, name='simtimeExtended')
continueRun = QtCore.pyqtSignal(float, float, name='continueRun')
def __init__(self, *args, **kwargs):
QtGui.QWidget.__init__(self, *args, **kwargs)
self.simulationInterval = None
self.updateInterval = None
self.runTime = None
self.modelRoot = None
self.dataRoot = None
self.runner = Runner()
self.resetAndRunAction = None
self.stopAction = None
self.continueAction = None
self.preferences = preferences
self.currentSimulationRuntime = None
self.modelType = None
self.simulationRuntime = None
self.schedulerToolBar = self.getSchedulerToolBar()
self.runner.simulationProgressed.connect(self.updateCurrentSimulationRuntime)
self.continueFlag = False
self.preferences.applyChemicalSettings.connect(self.resetSimulation)
def updateCurrentSimulationRuntime(self, time):
self.currentSimulationRuntime.setText(str(time))
def getToolBars(self):
return [self.schedulerToolBar]
def getSchedulerToolBar(self):
bar = QToolBar("Run", self)
self.resetAction = bar.addAction(
QIcon( os.path.join( config.MOOSE_ICON_DIR, 'reset.png' ) )
, 'Reset'
, self.resetSimulation
)
self.resetAction.setToolTip('Reset simulation.')
self.runAction = bar.addAction(
QIcon( os.path.join( config.MOOSE_ICON_DIR, 'run.png') )
, 'Run'
, self.runSimulation
)
self.runAction.setToolTip('Run simulation.')
self.stopAction = bar.addAction(
QIcon( os.path.join( config.MOOSE_ICON_DIR, 'stop.png') )
, 'Stop'
, self.runner.togglePauseSimulation
)
self.stopAction.setToolTip('Stop simulation.')
bar.addSeparator()
runtimeLabel = QLabel('Run for')
self.simulationRuntime = QLineEdit()
self.simulationRuntime.setValidator(QDoubleValidator())
self.simulationRuntime.setFixedWidth(75)
bar.addWidget(runtimeLabel)
bar.addWidget(self.simulationRuntime)
bar.addWidget(QLabel(' (s)'))
bar.addSeparator()
#: current time
self.currentSimulationRuntime = QLineEdit() # 6 digits
self.currentSimulationRuntime.setToolTip('Current simulation runtime.')
self.currentSimulationRuntime.setFixedWidth(75)
self.currentSimulationRuntime.setValidator(QDoubleValidator())
self.currentSimulationRuntime.setText("0.0")
self.currentSimulationRuntime.setReadOnly(True)
# self.runner.currentTime.connect(self.currentTimeWidget.display)
bar.addWidget(QLabel("Current Time : "))
bar.addWidget(self.currentSimulationRuntime)
bar.addWidget(QLabel(" (s)"))
bar.addSeparator()
self.preferencesButton = QToolButton()
self.preferencesButton.setText("Preferences")
self.preferencesButton.clicked.connect(self.preferencesToggler)
bar.addWidget(self.preferencesButton)
return bar
def continueSimulation(self):
self.runner.continueSimulation( self.runTime
, self.updateInterval
, self.simulationInterval
)
self.simulationRuntime.setText(str(float(self.simulationRuntime.text()) + self.runTime))
def resetSimulation(self):
self.setParameters()
try:
self.runtime = float(runtime)
except:
self.runtime = 100.0
# print(self.runTime)
# print(self.updateInterval)
# print(self.simulationInterval)
self.currentSimulationRuntime.setText("0.0")
self.checkConsistency()
# self.preferences.setChemicalClocks()
self.simulationRuntime.setText(str(self.runTime))
self.runner.resetSimulation( self.runTime
, self.updateInterval
, self.simulationInterval
)
self.continueFlag = False
def runSimulation(self):
if self.modelType == CHEMICAL_MODEL:
compt = moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
if not moose.exists(compt[0].path+'/stoich'):
chemPref = self.preferences.getChemicalPreferences()
solver = chemPref["simulation"]["solver"]
addSolver(self.modelRoot,solver)
status = self.solverStatus()
#print "status ",status
# if status != 0 or status == -1:
# return
if status == None or int(status) == -1 or int(status) == 0:
#allow the model to Run
pass
else:
# if something is dangling or solver is not set then return
return
runtime = str(self.simulationRuntime.text())
try:
self.runtime = float(runtime)
except:
self.runtime = 100.0
self.simulationRuntime.setText("100.0")
self.checkConsistency()
self.continueSimulation = True
self.runner.runSimulation(self.runtime)
def setParameters(self):
if self.modelType == ELECTRICAL_MODEL:
self.setElectricalParameters()
elif self.modelType == CHEMICAL_MODEL:
self.setChemicalParameters()
def setChemicalParameters(self):
chemicalPreferences = self.preferences.getChemicalPreferences()
self.preferences.initializeChemicalClocks()
self.updateInterval = chemicalPreferences["simulation"]["gui-update-interval"]
self.simulationInterval = chemicalPreferences["simulation"]["simulation-dt"]
if str(self.simulationRuntime.text()) == "":
self.simulationRuntime.setText(str(chemicalPreferences["simulation"]["default-runtime"]))
self.runTime = float(self.simulationRuntime.text())
self.solver = chemicalPreferences["simulation"]["solver"]
def setElectricalParameters(self):
electricalPreferences = self.preferences.getElectricalPreferences()
self.preferences.initializeElectricalClocks()
self.updateInterval = electricalPreferences["simulation"]["gui-update-interval"]
self.simulationInterval = electricalPreferences["simulation"]["simulation-dt"]
if str(self.simulationRuntime.text()) == "":
self.simulationRuntime.setText(str(electricalPreferences["simulation"]["default-runtime"]))
self.runTime = float(self.simulationRuntime.text())
self.solver = electricalPreferences["simulation"]["solver"]
def checkConsistency(self):
if self.updateInterval < self.simulationInterval :
self.updateInterval = self.simulationInterval
if self.runTime < self.updateInterval :
self.runTime = self.updateInterval
return True
def solverStatus(self):
compt = moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
if not moose.exists(compt[0].path+'/stoich'):
return None
else:
stoich = moose.Stoich(compt[0].path+'/stoich')
status = int(stoich.status)
# print("Status =>", status)
if status == -1:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Reaction path not yet assigned.\n ")
return -1
if status == 1:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in a Reac or Enz.\n ")
return 1
elif status == 2:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz.\n ")
return 2
elif status == 3:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing substrates as well as reactants.\n ")
return 3
elif status == 4:
QtGui.QMessageBox.warning(None,"Could not Run the model"," Warning: Compartment not defined.\n ")
return 4
elif status == 8:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Neither Ksolve nor Dsolve defined.\n ")
return 8
elif status == 16:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: No objects found on path.\n ")
return 16
elif status == 0:
print("Successfully built stoichiometry matrix.\n ")
# moose.reinit()
return 0
def __getAdvanceOptionsButton(self):
icon = QtGui.QIcon(os.path.join(config.settings[config.KEY_ICON_DIR],'arrow.png'))
# self.advancedOptionsButton.setIcon(QtGui.QIcon(icon))
# self.advancedOptionsButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon );
return self.advancedOptionsButton
def preferencesToggler(self):
visibility = not self.preferences.getView().isVisible()
self.preferences.getView().setVisible(visibility)
def continueSlot(self):
pass
def updateCurrentTime(self):
sys.stdout.flush()
self.currentTimeWidget.dispay(str(moose.Clock('/clock').currentTime))
def updateTextFromTick(self, tickNo):
tick = moose.vector('/clock/tick')[tickNo]
widget = self.tickListWidget.layout().itemAtPosition(tickNo + 1, 1).widget()
if widget is not None and isinstance(widget, QtGui.QLineEdit):
widget.setText(str(tick.dt))
def updateFromMoose(self):
"""Update the tick dt from the tick objects"""
ticks = moose.vector('/clock/tick')
# Items at position 0 are the column headers, hence ii+1
for ii in range(ticks[0].localNumField):
self.updateTextFromTick(ii)
self.updateCurrentTime()
def getSimTime(self):
try:
time = float(str(self.simtimeEdit.text()))
return time
except ValueError as e:
QtGui.QMessageBox.warning(self, 'Invalid value', 'Specified runtime was meaningless.')
return 0
def setDataRoot(self, root='/data'):
self.dataRoot = moose.element(root).path
def setModelRoot(self, root='/model'):
self.modelRoot = moose.element(root).path
self.setModelType()
def setModelType(self):
if moose.exists(self.modelRoot + "/model/cells"):
self.modelType = ELECTRICAL_MODEL
else:
self.modelType = CHEMICAL_MODEL
self.resetSimulation()
class SchedulingWidget(QWidget):
"""Widget for scheduling.
Important member fields:
runner - object to run/pause/continue simulation. Whenever
`updateInterval` time has been simulated this object sends an
`update()` signal. This can be connected to other objects to
update their data.
SIGNALS:
resetAndRun(tickDt, tickTargets, simtime, updateInterval)
tickDt: dict mapping tick nos to dt
tickTargets: dict mapping ticks to target paths
simtime: total simulation runtime
updateInterval: interval between update signals are to be emitted.
simtimeExtended(simtime)
emitted when simulation time is increased by user.
"""
resetAndRun = QtCore.pyqtSignal(dict,
dict,
float,
float,
name='resetAndRun')
simtimeExtended = QtCore.pyqtSignal(float, name='simtimeExtended')
continueRun = QtCore.pyqtSignal(float, float, name='continueRun')
def __init__(self, *args, **kwargs):
QWidget.__init__(self, *args, **kwargs)
self.simulationInterval = None
self.updateInterval = None
self.runTime = None
self.modelRoot = None
self.dataRoot = None
self.runner = Runner()
self.resetAndRunAction = None
self.stopAction = None
self.continueAction = None
self.preferences = preferences
self.currentSimulationRuntime = None
self.modelType = None
self.simulationRuntime = None
self.schedulerToolBar = self.getSchedulerToolBar()
self.runner.simulationProgressed.connect(
self.updateCurrentSimulationRuntime)
self.continueFlag = False
self.preferences.applyChemicalSettings.connect(self.resetSimulation)
def updateCurrentSimulationRuntime(self, time):
self.currentSimulationRuntime.setText(str(time))
def getToolBars(self):
return [self.schedulerToolBar]
def getSchedulerToolBar(self):
bar = QToolBar("Run", self)
self.resetAction = bar.addAction(
QtGui.QIcon(os.path.join(config.MOOSE_ICON_DIR, 'reset.png')),
'Reset', self.resetSimulation)
self.resetAction.setToolTip('Reset simulation.')
self.runAction = bar.addAction(
QtGui.QIcon(os.path.join(config.MOOSE_ICON_DIR, 'run.png')), 'Run',
self.runSimulation)
self.runAction.setToolTip('Run simulation.')
self.stopAction = bar.addAction(
QtGui.QIcon(os.path.join(config.MOOSE_ICON_DIR, 'stop.png')),
'Stop', self.runner.togglePauseSimulation)
self.stopAction.setToolTip('Stop simulation.')
bar.addSeparator()
runtimeLabel = QLabel('Run for')
self.simulationRuntime = QLineEdit()
self.simulationRuntime.setValidator(QtGui.QDoubleValidator())
self.simulationRuntime.setFixedWidth(75)
bar.addWidget(runtimeLabel)
bar.addWidget(self.simulationRuntime)
bar.addWidget(QLabel(' (s)'))
bar.addSeparator()
#: current time
self.currentSimulationRuntime = QLineEdit() # 6 digits
self.currentSimulationRuntime.setToolTip('Current simulation runtime.')
self.currentSimulationRuntime.setFixedWidth(75)
self.currentSimulationRuntime.setValidator(QtGui.QDoubleValidator())
self.currentSimulationRuntime.setText("0.0")
self.currentSimulationRuntime.setReadOnly(True)
# self.runner.currentTime.connect(self.currentTimeWidget.display)
bar.addWidget(QLabel("Current Time : "))
bar.addWidget(self.currentSimulationRuntime)
bar.addWidget(QLabel(" (s)"))
bar.addSeparator()
self.preferencesButton = QToolButton()
self.preferencesButton.setText("Preferences")
self.preferencesButton.clicked.connect(self.preferencesToggler)
bar.addWidget(self.preferencesButton)
return bar
def continueSimulation(self):
self.runner.continueSimulation(self.runTime, self.updateInterval,
self.simulationInterval)
self.simulationRuntime.setText(
str(float(self.simulationRuntime.text()) + self.runTime))
def resetSimulation(self):
self.setParameters()
try:
self.runtime = float(runtime)
except:
self.runtime = 100.0
# print(self.runTime)
# print(self.updateInterval)
# print(self.simulationInterval)
self.currentSimulationRuntime.setText("0.0")
self.checkConsistency()
# self.preferences.setChemicalClocks()
self.simulationRuntime.setText(str(self.runTime))
self.runner.resetSimulation(self.runTime, self.updateInterval,
self.simulationInterval)
self.continueFlag = False
def runSimulation(self):
if self.modelType == CHEMICAL_MODEL:
compt = moose.wildcardFind(self.modelRoot + '/##[ISA=ChemCompt]')
if not moose.exists(compt[0].path + '/stoich'):
chemPref = self.preferences.getChemicalPreferences()
solver = chemPref["simulation"]["solver"]
mooseAddChemSolver(self.modelRoot, solver)
status = self.solverStatus()
#print "status ",status
# if status != 0 or status == -1:
# return
if status == None or int(status) == -1 or int(status) == 0:
#allow the model to Run
pass
else:
# if something is dangling or solver is not set then return
return
runtime = str(self.simulationRuntime.text())
try:
self.runtime = float(runtime)
except:
self.runtime = 100.0
self.simulationRuntime.setText("100.0")
self.checkConsistency()
self.continueSimulation = True
self.runner.runSimulation(self.runtime)
def setParameters(self):
if self.modelType == ELECTRICAL_MODEL:
self.setElectricalParameters()
elif self.modelType == CHEMICAL_MODEL:
self.setChemicalParameters()
def setChemicalParameters(self):
chemicalPreferences = self.preferences.getChemicalPreferences()
self.preferences.initializeChemicalClocks()
self.updateInterval = chemicalPreferences["simulation"][
"gui-update-interval"]
self.simulationInterval = chemicalPreferences["simulation"][
"simulation-dt"]
if str(self.simulationRuntime.text()) == "":
self.simulationRuntime.setText(
str(chemicalPreferences["simulation"]["default-runtime"]))
self.runTime = float(self.simulationRuntime.text())
self.solver = chemicalPreferences["simulation"]["solver"]
def setElectricalParameters(self):
electricalPreferences = self.preferences.getElectricalPreferences()
self.preferences.initializeElectricalClocks()
self.updateInterval = electricalPreferences["simulation"][
"gui-update-interval"]
self.simulationInterval = electricalPreferences["simulation"][
"simulation-dt"]
if str(self.simulationRuntime.text()) == "":
self.simulationRuntime.setText(
str(electricalPreferences["simulation"]["default-runtime"]))
self.runTime = float(self.simulationRuntime.text())
self.solver = electricalPreferences["simulation"]["solver"]
def checkConsistency(self):
if self.updateInterval < self.simulationInterval:
self.updateInterval = self.simulationInterval
if self.runTime < self.updateInterval:
self.runTime = self.updateInterval
return True
def solverStatus(self):
compt = moose.wildcardFind(self.modelRoot + '/##[ISA=ChemCompt]')
if not moose.exists(compt[0].path + '/stoich'):
return None
else:
stoich = moose.Stoich(compt[0].path + '/stoich')
status = int(stoich.status)
# Flag to track status of Stoich object.
# -1: No path yet assigned.
# 0: Success
# 1: Warning: Missing reactant in Reac or Enz
# 2: Warning: Missing substrate in MMenz
# 4: Warning: Compartment not defined
# 8: Warning: Neither Ksolve nor Dsolve defined
# 16: Warning: No objects found on path
# print("Status =>", status)
if status == 1 or status == 2:
nameRE = "\n\nclassName --> parentName/groupName --> name "
for res in moose.wildcardFind(self.modelRoot +
'/##[ISA=ReacBase],' +
self.modelRoot +
'/##[ISA=EnzBase]'):
if not len(res.neighbors["sub"]) or not len(
res.neighbors["prd"]):
nameRE = nameRE + "\n " + res.className + " --> " + res.parent.name + " --> " + res.name
if status == -1:
QMessageBox.warning(
None, "Could not Run the model",
"Warning: Reaction path not yet assigned.\n ")
return -1
if status == 1:
#QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in a Reac or Enz.\n ")
QMessageBox.warning(
None, "Could not Run the model",
"Warning: Missing a reactant in %s " % (nameRE))
return 1
elif status == 2:
QMessageBox.warning(
None, "Could not Run the model",
"Warning: Missing a substrate in an MMenz %s " % (nameRE))
#QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz.\n ")
return 2
elif status == 4:
QMessageBox.warning(None, "Could not Run the model",
" Warning: Compartment not defined.\n ")
return 4
elif status == 8:
QMessageBox.warning(
None, "Could not Run the model",
"Warning: Neither Ksolve nor Dsolve defined.\n ")
return 8
elif status == 16:
QMessageBox.warning(None, "Could not Run the model",
"Warning: No objects found on path.\n ")
return 16
elif status == 0:
print("Successfully built stoichiometry matrix.\n ")
# moose.reinit()
return 0
def preferencesToggler(self):
visibility = not self.preferences.getView().isVisible()
self.preferences.getView().setVisible(visibility)
def continueSlot(self):
pass
def updateCurrentTime(self):
sys.stdout.flush()
self.currentTimeWidget.dispay(str(moose.Clock('/clock').currentTime))
def updateTextFromTick(self, tickNo):
tick = moose.vector('/clock/tick')[tickNo]
widget = self.tickListWidget.layout().itemAtPosition(tickNo + 1,
1).widget()
if widget is not None and isinstance(widget, QLineEdit):
widget.setText(str(tick.dt))
def updateFromMoose(self):
"""Update the tick dt from the tick objects"""
ticks = moose.vector('/clock/tick')
# Items at position 0 are the column headers, hence ii+1
for ii in range(ticks[0].localNumField):
self.updateTextFromTick(ii)
self.updateCurrentTime()
def getSimTime(self):
try:
time = float(str(self.simtimeEdit.text()))
return time
except ValueError:
QMessageBox.warning(self, 'Invalid value',
'Specified runtime was meaningless.')
return 0.0
def setDataRoot(self, root='/data'):
self.dataRoot = moose.element(root).path
def setModelRoot(self, root='/model'):
self.modelRoot = moose.element(root).path
self.setModelType()
def setModelType(self):
if moose.exists(self.modelRoot + "/model/cells"):
self.modelType = ELECTRICAL_MODEL
else:
self.modelType = CHEMICAL_MODEL
self.resetSimulation()